==Background==
I suffer from crippling joint pain. When it attacks my wrists I can't even hold a cup of coffee with one hand. I feel every beat of my heart as a pulse of pain in my wrists. It's not carpal tunnel though so I'm not sure how that plays in to this opinion for your situation but some co-workers have told me this holds for their CT too.
==Mouse==
First, your mouse is your worst enemy. The buttons on your mouse are crappy and way too stiff. The constant small motion of clicking, clicking, clicking from the exact same position just sets you up for a fast increase in pain when you go back to your keyboard. I've tried mousing left and right handed to spread the pain. You can hook up two mice at the same time with no change to functionality and you get used to using your other hand fairly quickly. Still not much good though! I've tried trackballs, sideways ergonomic mice, and everything else you can think of. They all suffer from the crappy stiff minimal travel buttons. The thing that works best for me is a touchpad ... and learning to use a light tap! My favorite stand alone is the Logitech Wireless T650 (http://www.logitech.com/en-us/product/touchpad-t650). Tracks well, handles very light taps, and is nice and big for a touchpad. Next is the Adesso Smart Cat 410 (http://www.adesso.com/products/product-detail-97.html). It's wired and not as big, but it has edges and I like the ability to bump up along the right edge and scroll with one finger rather than the Logitech two finger scroll. It gets the scroll right a bit more consistently. Either of these touchpad allow me to use a keyboard longer.
==Keyboards and Switches==
The Cherry switches are ALL too stiff. The reds and browns are best with the reds having an activation force of 45 cN. The browns are smoother but have a 55 cN activation force. And none of them bottom out nicely for me. You can use little o-rings to help a bit. The best way to try all the Cherry switches is with this little device here: http://www.amazon.com/gp/product/B00N6DXTW4. But I couldn't come up with any keyboard/configuration that really helped me. I've got a good dozen high end mechanical keyboards sitting in a closet. And I found little difference between brands, keyboard layouts, "ergonomic keyboards", etc.
Topre makes what might be a good solution in that they make keyboards with variable key weights depending on key positions. Their boards are about $250 but I've not tried one as their home keys still seem too great a force for me at this point.
For me, my go to keyboard is the Adesso SlimTouch 4400 series (http://www.adesso.com/products/product-detail-82.html). It comes in both USB and wireless versions. The keys are cheapish membrane switches and are still too stiff, but the travel and bottoming out are very good. Unfortunately, it's a bit hit or miss as any particular keyboard might be stiffer than one in another batch. Not sure why though. It also has a built in reasonable quality touchpad for your right hand. There are some new Adessos that I've not tried but look interesting. For example http://www.adesso.com/products/product-detail-149.html. I probably should give it a go.
The best keyboard I've tried is the Razor Deathstalker Ultimate (http://www.razerzone.com/gaming-keyboards-keypads/razer-deat...). The key travel and bottoming out are excellent. The activation force is still too high though. However, this is a silly expensive keyboard because of the built in touchpad/display which, for all the hype and engineering effort they put into it, is a crap touchpad. The sheer number of times a tap isn't turned into a touch or turned into a double tap makes this thing a joke. All the time and effort razer must have spent making the little display do everything imaginable EXCEPT making it work as a touchpad. WTF razer!
Finally, it's worth it to look in to Dragon for voice to text. It's worthless for programming but can help take joint burden away for long text only things. Speaking of which ... I'll stop here.